Re: abf: multiple distance

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Nov 30 2007 - 11:44:39 CST

Dear Vlad,

> You mentioned in this reply to Luca that you could point him to few
> papers that describe how to derive the gradient of a reaction
> coordinated depending on several distances in Cartesian coordinates.
>
> Could you write me the citations of these paper(s)?

I didn't mean anything specific about coordinates depending on several
distances, or about how to derive gradients.
I was thinking of papers that explain how one can measure a force and
apply a bias using the gradient (and another vector, the "inverse
gradient"), and related issues. They are mainly the original ABF
article by Darve and Pohorille (JCP 2001), our NAMD/ABF paper (Henin
and Chipot, JCP 2004) and a few others that those two cite. I can give
you more details if you are interested in anything specific.

There are actually several ways to estimate the force, but in any case
one has to compute the gradient to apply the bias, and the most
practical way is still analytical for all but extremely complicated
coordinates.

Jerome

> Jerome Henin wrote:
>
> >Hi Luca,
> >
> >On Nov 30, 2007 4:22 AM, luca <bellucci14_at_unisi.it> wrote:
> >
> >
> >>On Friday 30 November 2007 00:37:54 you wrote:
> >>Hi Jerome,
> >>Thank for replay.
> >>
> >>
> >>>Dear Luca,
> >>>If your "more advanced reaction coordinate" is a single variable that
> >>>depends on several distances, you just have to work out a few
> >>>equations (mostly the gradient of that variable in Cartesian
> >>>coordinates). I can point you to a few papers if you need it.
> >>>
> >>>
> >>I am interested on this argument. I have been reading some article this week , but
> >>I think that this is a difficult work to implement ...in fast and easy way.
> >>
> >>
> >
> >That is true. Implementing new coordinates takes some time and effort,
> >except in the simplest cases. That is why we encourage people who
> >write them to contribute them so that others in the community do not
> >duplicate the work.
> >
> >
> >
> >>>If what you really want is to define a multidimensional free energy
> >>>surface, function of several distances, then the NAMD ABF code cannot
> >>>currently do that.
> >>>
> >>>
> >>Yes, I'm sorry I had this in mind .
> >>
> >>
> >>>We are working on making this possible in future
> >>>versions, but there is no release schedule yet.
> >>>
> >>>
> >>Ok. I will see http://www.edam.uhp-nancy.fr/ABF/index.html
> >>At this moment I can run multiple md with different reaction coordinates and
> >>make FES manually. Do You have a reference/suggestion for this approach?
> >>
> >>
> >
> >I can see two cases:
> >1) The different coordinates are not significantly correlated. In this
> >case, the free energy will be additive:
> >A(x1, x2, x3) = A1(x1) + A2(x2) + A3(x3)
> >and all the information is contained in the 1-D profiles.
> >
> >2) The coordinates are correlated. That can still be treated if you
> >can define discrete states for most of the coordinates, e.g. if the
> >1-D profiles have a small number of free energy basins. Then you could
> >compute 1-D PMFs with all other coordinates restrained to a specific
> >state, and repeat this procedure for all states you consider
> >interesting.
> >Of course, this only works if you have a good intuitive understanding
> >of the system already, and it gets impractical if there are many
> >coordinates/states, but it may help get "semi-quantitative" results.
> >
> >Jerome
> >
> >
> >
> >
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
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>
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>
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